omero-vitessce 0.1.0

OMERO Vitessce multimodal data viewer plugin for OMERO.web

OMERO.omero_vitessce

OMERO Vitessce multimodal data viewer.

Installation

Install omero_vitessce in mode as follows:

# within your python venv:
cd omero-vitessce
pip install -e .

Add the app to the omero.web.apps setting:

omero config append omero.web.apps '"omero_vitessce"'

Add omero_vitessce as a tab in the right-hand-side panel:

omero config append omero.web.ui.right_plugins '["Vitessce", "omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html", "vitessce_tab"]'

Add the omero web address (replace ´'"http://localhost:4080"'´ with your address):

omero config set omero.web.omero_vitessce.serveraddress '"http://localhost:4080"'

Now restart OMERO.web as normal for the configuration above to take effect.

Usage

Right-hand-side panel:

• Prexisting config files
• Autogenerating config file:

Open-with:

COMING SOON!

Development

Sources

• cookiecutter-omero-webapp: https://github.com/ome/cookiecutter-omero-webapp
• react_webapp from omero-web-apps-examples: https://github.com/ome/omero-web-apps-examples/tree/master/react-webapp
• Vitessce python package (will be used for generating config files) http://python-docs.vitessce.io/

React web app

omero_vitessce web app

We serve a custom version of the vitesce app: http://vitessce.io/

The app sets up a vitessce view configured through a text file in json format: http://vitessce.io/docs/view-config-json/

The configuration file is taken from the ?config url parameter.

Installation

This project was created with Create React App.

You can run this project in development mode or as an OMERO.web Django app.

To get started:

cd vitessce_app
npm install

In the project directory, you can run:

npm start

Runs the app in the development mode.
Open http://localhost:3000 to view it in the browser.

The page will reload if you make edits.
You will also see any lint errors in the console.

npm run build

Builds the app for production to the build folder and copies the html and static files to the Django app in vitessce app. See the deploy_build.sh script.

You also need to install the app into your omero-web environment:

# cd to the root of the repo
pip install -e .

You will need to have the app configured in your OMERO.web install:

  omero config append omero.web.apps '"omero_vitessce"'
  omero config append omero.web.ui.right_plugins '["Vitessce", "omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html", "vitessce_tab"]'
  omero config set omero.web.omero_vitessce.serveraddress '"http://localhost:4080"'

It bundles React in production mode and optimizes the build for the best performance.

See the Create React App section about deployment for more information.